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Top Forums Shell Programming and Scripting Newbie wanting help with a script Post 302556465 by foyn on Sunday 18th of September 2011 04:11:38 PM
Old 09-18-2011
Thank you. Have done that now and the first part is now working (clustalw), but now I get the following error:


PHYLIP-Alignment file created [.output]


ERROR: the input file does not seem to be a valid Phylip file
collapse1.5(1635) malloc: *** mmap(size=140737488355328) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug


Seems like the output file is not named correctly so collapse1.5 don't find the input. Is there something wrong with my INPUT_FILE variable?

---------- Post updated at 09:11 PM ---------- Previous update was at 09:07 PM ----------

Fixed it
 

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CHECKBASHISMS(1)					      General Commands Manual						  CHECKBASHISMS(1)

NAME
checkbashisms - check for bashisms in /bin/sh scripts SYNOPSIS
checkbashisms script ... checkbashisms --help|--version DESCRIPTION
checkbashisms, based on one of the checks from the lintian system, performs basic checks on /bin/sh shell scripts for the possible presence of bashisms. It takes the names of the shell scripts on the command line, and outputs warnings if possible bashisms are detected. Note that the definition of a bashism in this context roughly equates to "a shell feature that is not required to be supported by POSIX"; this means that some issues flagged may be permitted under optional sections of POSIX, such as XSI or User Portability. In cases where POSIX and Debian Policy disagree, checkbashisms by default allows extensions permitted by Policy but may also provide options for stricter checking. OPTIONS
--help, -h Show a summary of options. --newline, -n Check for "echo -n" usage (non POSIX but required by Debian Policy 10.4.) --posix, -p Check for issues which are non POSIX but required to be supported by Debian Policy 10.4 (implies -n). --force, -f Force each script to be checked, even if it would normally not be (for instance, it has a bash or non POSIX shell shebang or appears to be a shell wrapper). --extra, -x Highlight lines which, whilst they do not contain bashisms, may be useful in determining whether a particular issue is a false posi- tive which may be ignored. For example, the use of "$BASH_ENV" may be preceded by checking whether "$BASH" is set. --version, -v Show version and copyright information. EXIT VALUES
The exit value will be 0 if no possible bashisms or other problems were detected. Otherwise it will be the sum of the following error val- ues: 1 A possible bashism was detected. 2 A file was skipped for some reason, for example, because it was unreadable or not found. The warning message will give details. SEE ALSO
lintian(1). AUTHOR
checkbashisms was originally written as a shell script by Yann Dirson <dirson@debian.org> and rewritten in Perl with many more features by Julian Gilbey <jdg@debian.org>. DEBIAN
Debian Utilities CHECKBASHISMS(1)
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